SAN FRANCISCO -- Colin Kaepernick thinks he has a secret weapon, one he'll deploy in Sunday's season opener against the Green Bay Packers.

It's his brain.

Not his blowtorch of an arm. Not his sprinter legs. Not the leadership skills that led to his newly appointed captaincy.

Kaepernick, 25, touts his mental preparation as his greatest and most overlooked asset entering his first full season as the 49ers' starting quarterback. Forgive him if his football I.Q. didn't come across on the au-naturel ESPN The Magazine cover that gained him much attention this offseason.

San Francisco 49ers' quarterback Colin Kaepernick (7) is pressured by Minnesota Vikings' Brian Robinson (96) in the first quarter of their preseason game at Candlestick Park in San Francisco, Calif., on Sunday, Aug. 25, 2013. (Susan Tripp Pollard/Bay Area News Group)

"A lot of people, they'll see commercials or photo shoots or whatever and say, 'Why isn't he working? Why isn't he getting prepared?'," Kaepernick said. "They don't realize before I did any one of those things, I schedule all that around my workouts and what I have to do to get ready for football."

That prep work entails much more than his 6 a.m. sprints on the practice field. Away from his newfound-celebrity spotlight, Kaepernick reverts into a football nerd, studying all aspects he can behind the gray doors of the 49ers' training complex.

"He's definitely a very intelligent guy, and that gets lost in the fact he's athletic and has a lot of talent," center Jonathan Goodwin said. "There's been a lot on his plate and he's been able to handle it from Day 1."

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Day 1 as a starter came last November, when Kaepernick replaced a concussed Alex Smith against the Bears at Candlestick Park on Monday Night Football. In his 10th career start, Kaepernick brought the 49ers to the threshold of a Super Bowl XLVII victory, only to see his final three passes fall incomplete from the Baltimore Ravens' 5-yard line.

Carrying a clipboard for 1½ seasons alongside the cerebral Smith was time well spent, according to offensive coordinator Greg Roman.

"When Kap first got here, Alex was so far ahead of him that I think Kap silently to himself said, 'Whoa, if I'm going to do what he does, I've got to know what he knows," Roman said. "He really set off to learn and get comfortable and proficient and speak the lingo."

Kaepernick was no dumb jock. Reportedly, his Wonderlic score at the 2011 scouting combine was 37 (average for quarterbacks: 24). He carried a 4.1 grade-point average at Pittman High in Turlock, and while he kept his grades up at the University of Nevada, that's where his football I.Q. began to soar.

"In high school, you just call a lot of plays and you go out, you run them and, for the most part, you try to hit the open guy," Kaepernick said. "When you get to college, you start having progressions, you have to go through reads, read coverages and get your offense in the right situation.

"Moving on to the NFL, it's another big step as far as what defenses are going to do to try to attack you, and how can you counter that? How can you be prepared and put your team in the best situation?"

To set up the 49ers for a Super Bowl encore, Kaepernick has kept his body in tiptop shape (see: ESPN's body issue). He's established chemistry with new teammates (see: Boldin, Anquan). He's sat through -- and spoken up often -- in study sessions with Roman, Jim Harbaugh and quarterbacks coach Geep Chryst.

"Very impressed with how he goes about his job," Harbaugh said. "He takes on a great responsibility there as the quarterback: to study the opponent, to study their personnel, to study the ready list, to study the game plan, contribute to the game plan, make suggestions.

"He's a very inquisitive guy that wants to know all the details."

When Kaepernick's mental makeup got called into question last month on the NFL Network, Cris Collinsworth of NBC Sports responded on Twitter: "I totally disagree with what I just heard. Colin Kaepernick is very intelligent. His play and decision making reflect that."

The 49ers' introduction of iPad playbooks this training camp allowed Kaepernick to study from anywhere, even if most of his work is done in the 49ers' facility

"It's something I'm constantly going over in my mind, whether I'm here or at home," Kaepernick said. "I'm always going over different scenarios, different things, just to make sure when I step out on the field, it's something I don't have to think about."